Migraine, tension-type headache (TTH) and headaches attributed to temporomandibular disorders (TMD) are prevalent in patients with TMD-pain. The objective was to describe the course of headache complaints as compared to the course of TMD complaints in TMD-pain patients with headache during usual care multidisciplinary treatment for TMD. This was a 12-week longitudinal observational study following adults with TMD-pain and headache during a usual-care multidisciplinary TMD-treatment. The Graded Chronic Pain Scale was used for both TMD and headache to measure pain-related disability (primary outcome measure), pain intensity, days with pain and days experiencing disability (secondary outcome measures). Stratified for the headache type, general linear modelling for repeated measures was used to analyze changes over time in the TMD complaints and the headache complaints. TMD-pain patients with migraine (n = 22) showed significant decrease of pain-related disability for both TMD and headache complaints over time. No difference in the effect over time was found between the two complaints. Patients with TMD-pain and TTH (n = 21) or headache attributed to TMD (n = 17) did not improve in disability over time. For the secondary outcome measures, the results were equivocal. In conclusion, TMD-pain patients with migraine, improvement in TMD-related disability was comparable to headache-related disability for TMD-pain patients with TTH or with headache attributed to TMD, no improvements in disability were found.